- User Guide
FIRST is a model-based segmentation/registration tool. The shape/appearance models used in FIRST are constructed from manually segmented images provided by the Center for Morphometric Analysis (CMA), MGH, Boston. The manual labels are parameterized as surface meshes and modelled as a point distribution model. Deformable surfaces are used to automatically parameterize the volumetric labels in terms of meshes; the deformable surfaces are constrained to preserve vertex correspondence across the training data. Furthermore, normalized intensities along the surface normals are sampled and modelled. The shape and appearance model is based on multivariate Gaussian assumptions. Shape is then expressed as a mean with modes of variation (principal components). Based on our learned models, FIRST searches through linear combinations of shape modes of variation for the most probable shape instance given the observed intensities in your T1 image.
For more information on FIRST, see the NeuroImage paper (detailed in References).
The following reference is the main journal paper describing FIRST:
Patenaude, B., Smith, S.M., Kennedy, D., and Jenkinson M. A Bayesian Model of Shape and Appearance for Subcortical Brain NeuroImage, 56(3):907-922, 2011.
There is also a thesis relating to FIRST that contains some more technical details:
Brian Patenaude. Bayesian Statistical Models of Shape and Appearance for Subcortical Brain Segmentation. D.Phil. Thesis. University of Oxford. 2007.
FIRST Training Data Contributors
We are very grateful for the training data for FIRST, particularly to David Kennedy at the CMA, and also to: Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier, Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein, Department of Psychiatry of Harvard Medical School; Barry Kosofsky, Weill Cornell Medical Center.